GEO series

Comparative analysis of gene expression upon DMSO-induced differentiation of hepatoma cell lines [Dif]

GSE288204 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/04/23 Platform GPL21290

At a glance

RNA-seq (gene expression) · human · 12 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Samples: 12 samples: 3 × HuH7.5-NTCP_Dif vs 3 × HuH7.5-NTCP_ND vs 3 × HuH7-NTCP_Dif vs 3 × HuH7-NTCP_NDGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: A novel in vitro system for simultaneous infections with hepatitis B, C, D and E virusesJHEP reports : innovation in hepatology · 2025

Summary (written by the submitters)

The liver, and more precisely hepatocytes, can be infected by several viruses such as hepatitis B (HBV), hepatitis D (HDV), hepatitis C (HCV), hepatitis E (HEV) viruses, with chronic infection leading to end-stage liver diseases. Since no in vitro model allowing multi-infections with the four viruses is reported, limited data are available on the interplay between those viruses as well as on the potential cross-reactivity of antivirals in multi-infection cases.

Read the full summary ↓

Here we showed that HuH7.5-NTCP cells can be partially differentiated into hepatocyte-like cells and genuinely replicate HBV, HDV, HCV and HEV for at least 4 weeks after mono or multiple infections. Additionally, we recapitulated the effect of known antivirals and found that FXR-agonists, also strongly inhibited HEV replication. Using HEV infected HuHep mice, we confirmed the antiviral effect of Vonafexor, the FXR agonist clinical candidate currently tested against HBV and HDV, highlighting FXR-ligands as potential broad acting antivirals. Here, we set-up the first in vitro model allowing multi-infections with hepatitis viruses that can be used for broad drug screening.

Published in

A novel in vitro system for simultaneous infections with hepatitis B, C, D and E viruses

Fouillé R, Verrier ER, De Meyer A et al. · JHEP reports : innovation in hepatology 2025 · PMID 40242313 · doi:10.1016/j.jhepr.2025.101383

This dataset

Open GSE288204 in finder → Find more human RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE288204_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1216558 and SRA study SRP560374. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40242313) ↗

Study design

3 × HuH7.5-NTCP_Dif vs 3 × HuH7.5-NTCP_ND vs 3 × HuH7-NTCP_Dif vs 3 × HuH7-NTCP_ND

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM8761216 HuH7.5-NTCP_Dif_1 HuH7.5-NTCP_Dif
GSM8761217 HuH7.5-NTCP_Dif_2 HuH7.5-NTCP_Dif
GSM8761218 HuH7.5-NTCP_Dif_3 HuH7.5-NTCP_Dif
GSM8761219 HuH7.5-NTCP_ND_1 HuH7.5-NTCP_ND
GSM8761220 HuH7.5-NTCP_ND_2 HuH7.5-NTCP_ND
GSM8761221 HuH7.5-NTCP_ND_3 HuH7.5-NTCP_ND
GSM8761222 HuH7-NTCP_Dif_1 HuH7-NTCP_Dif
GSM8761223 HuH7-NTCP_Dif_2 HuH7-NTCP_Dif
GSM8761224 HuH7-NTCP_Dif_3 HuH7-NTCP_Dif
GSM8761225 HuH7-NTCP_ND_1 HuH7-NTCP_ND
GSM8761226 HuH7-NTCP_ND_2 HuH7-NTCP_ND
GSM8761227 HuH7-NTCP_ND_3 HuH7-NTCP_ND

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